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1. Introduction
2. Topics
3. Genetic association studies
4. Typical design for an association study
5. SNP genotype data from an association study
6. Genome-wide association studies (1)
7. Genome-wide association studies (2)
8. Genome-wide association studies (3)
9. Graphical representation of one/two-stage design
10. Analyzing two-stage designs
11. Genome-wide false positive rate
12. Calculating power for two-stage designs
13. Stage 1: selecting SNPs for follow-up (1)
14. Stage 1: selecting SNPs for follow-up (2)
15. Stage 2: replication based analysis (1)
16. Stage 2: replication based analysis (2)
17. Stage 2: joint analysis (1)
18. Stage 2: joint analysis (2)
19. Replication-based and joint analysis critical values
20. Which analysis is more powerful?
21. Which is more powerful? - results
22. How power changes with proportion of samples?
23. Effect of pi-samples on power
24. How power changes with proportion of SNPs?
25. Effect of pi-markers on power
26. Between-stage heterogeneity influence on power
27. Effect of between-stage heterogeneity on power
28. Take home points
29. Designing optimal two-stage GWA studies
30. Assumptions
31. Determining the optimal two-stage design
32. One-stage power preserved in two-stage designs
33. Cost and power of two-stage designs: R = 1
34. Cost and power of two-stage designs: R = 5
35. Cost ratio changes optimal two-stage designs
36. What happens when cost ratio is misspecified?
37. Misspecifying cost ratio has minor effect
38. Strategies for further reducing GWA cost
39. Reduce cost by decresing pi-power
40. Reduce cost by relaxing alpha-marker
41. Increasing power by relaxing alpha-marker
42. Using custom arrays in stage 2
43. Custom array cost structure
44. Optimal two-stage designs using custom arrays
45. Custom array example
46. Admissible pi-markers
47. Comparing optimal designs
48. Summary (1)
49. Summary (2)
50. Acknowledgements
51. References

Topics Covered

• Introduction to genome-wide association studies (GWAs)
• Construction, analysis and power of two-stage GWAs
• Designing optimal two-stage GWAs
• Strategies for further reducing the cost of two-stage GWAs
• Handling custom arrays when designing optimal GWA

Links

Series:

• Genetic Epidemiology II

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Publication History

• Published on October 1, 2007

Financial Disclosures

• Dr. Andrew Skol has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.